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- Gutiérrez-Valencia, Juanita, et al.
(author)
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Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina
- 2022
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In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 39:1
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Journal article (peer-reviewed)abstract
- Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.
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| 2. |
- Horvath, Robert, 1988-
(author)
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Population genomic analyses of regulatory variation and selection in Brassicaceae species
- 2020
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Doctoral thesis (other academic/artistic)abstract
- The impact of selection on regulatory variation and the contribution of regulatory changes to phenotypic variation has long been debated in evolutionary genetics. Because cis-regulatory elements such as promoters and enhancers can be difficult to identify, it has been more challenging to quantify the impact of selection on variation in cis-regulatory regions than in protein-coding regions. In this thesis, I use genomic tools to investigate gene expression variation and selection in Brassicaceae species. First, I investigated the genomic impact of selection on putative cis-regulatory regions in the genome of the crucifer species Capsella grandiflora (Brassicaceae) (Paper I). I used an assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) to empirically identify putative cis-regulatory regions as those located in accessible chromatin regions (ACRs) in the genome of the crucifer species Capsella grandiflora. Based on whole-genome resequencing data from a natural population, I then showed that ACRs are under stronger purifying selection than other intergenic regions and that they are depleted for transposable element (TE) insertions and enriched for expression quantitative trait loci (eQTL), as would be expected if ACRs are enriched for functional elements affecting gene expression. Second, I explored how the location and silencing of transposable elements (TEs) affects selection against TEs (Paper II). Specifically, I tested a trade-off model on epigenetic TE silencing, according to which the positive effects of TE silencing on preventing TE movement conflict with negative effects of TE silencing on nearby gene expression. I found that TE silencing through the RNA-directed DNA methylation (RdDM) pathway affects selection against TEs close to genes in C. grandiflora, which is consistent with the trade-off model. Third, I used Arabidopsis thaliana single-cell expression data to investigate the relationship between gene body methylation (gbM) and transcriptional regulation (Paper III). I found that there was an indirect correlation between gbM and gene expression noise as well as a direct correlation between gbM and gene expression consistency and potentially intron retention in Arabidopsis thaliana. Fourth, I investigated the impact of demographic history on genomic signatures of selection at linked sites (linked selection) (Paper IV). This study revealed that neutral genetic diversity in C. grandiflora with a stable effective population size is influenced by linked selection whereas in Arabidopsis lyrata, which underwent a recent and strong bottleneck, neutral diversity is mainly affected by population size change. In summary, this thesis offers new insights into determinants of gene expression variation, selection on genomic features linked to gene expression alteration, as well as on the effect of demographic history on linked selection patterns in Brassicaceae.
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| 4. |
- Svantesson, Jasmine, et al.
(author)
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Shedding light on the non-operative treatment of the forgotten side of the knee: Rehabilitation of medial collateral ligament injuries - A systematic review
- 2024
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In: BMJ Open Sport and Exercise Medicine. - 2055-7647. ; 10
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Research review (peer-reviewed)abstract
- Objective The purpose of this study was to review the current literature regarding the non-operative treatment of isolated medial collateral ligament (MCL) injuries. Design Systematic review, registered in the Open Science Framework (https://doi.org/10.17605/OSF.IO/E9CP4). Data sources The Embase, MEDLINE and PEDro databases were searched; last search was performed on December 2023. Eligibility criteria Peer-reviewed original reports from studies that included information about individuals who sustained an isolated MCL injury with non-surgical treatment as an intervention, or reports comparing surgical with non-surgical treatment were eligible for inclusion. Included reports were synthesised qualitatively. Risk of bias was assessed with the Risk of Bias Assessment tool for Non-randomized Studies. Certainty of evidence was determined using the Grading of Recommendations Assessment Development and Evaluation. Results A total of 26 reports (1912 patients) were included, of which 18 were published before the year 2000 and 8 after. No differences in non-operative treatment were reported between grade I and II injuries, where immediate weight bearing and ambulation were tolerated, and rehabilitation comprised different types of strengthening exercises with poorly reported details. Some reports used immobilisation with a brace as a treatment method, while others did not use any equipment. The use of a brace and duration of use was inconsistently reported. Conclusion There is substantial heterogeneity and lack of detail regarding the non-operative treatment of isolated MCL injuries. This should prompt researchers and clinicians to produce high-quality evidence studies on the promising non-operative treatment of isolated MCL injuries to aid in decision-making and guide rehabilitation after MCL injury. Level of evidence Level I, systematic review.
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